qsvaR
This is the development version of qsvaR; for the stable release version, see qsvaR.
Generate Quality Surrogate Variable Analysis for Degradation Correction
Bioconductor version: Development (3.24)
The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.
Author: Joshua Stolz [aut]
, Hedia Tnani [ctb]
, Leonardo Collado-Torres [ctb]
, Nicholas J. Eagles [aut, cre]
Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com>
citation("qsvaR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("qsvaR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("qsvaR")| Introduction to qsvaR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, Coverage, DifferentialExpression, Normalization, Sequencing, Software, WorkflowStep |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2), SummarizedExperiment |
| Imports | dplyr, sva, stats, ggplot2, rlang, methods |
| System Requirements | |
| URL | https://github.com/LieberInstitute/qsvaR |
| Bug Reports | https://support.bioconductor.org/t/qsvaR |
See More
| Suggests | BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | qsvaR_1.17.0.tar.gz |
| Windows Binary (x86_64) | qsvaR_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | qsvaR_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | qsvaR_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/qsvaR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/qsvaR |
| Bioc Package Browser | https://code.bioconductor.org/browse/qsvaR/ |
| Package Short Url | https://bioconductor.org/packages/qsvaR/ |
| Package Downloads Report | Download Stats |